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Persistent homology

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https://www.readbyqxmd.com/read/27911727/role-of-the-bone-morphogenic-protein-pathway-in-developmental-haemopoiesis-and-leukaemogenesis
#1
REVIEW
Parto Toofan, Helen Wheadon
Myeloid leukaemias share the common characteristics of being stem cell-derived clonal diseases, characterised by excessive proliferation of one or more myeloid lineage. Chronic myeloid leukaemia (CML) arises from a genetic alteration in a normal haemopoietic stem cell (HSC) giving rise to a leukaemic stem cell (LSC) within the bone marrow (BM) 'niche'. CML is characterised by the presence of the oncogenic tyrosine kinase fusion protein breakpoint cluster region-abelson murine leukaemia viral oncogene homolog 1 (BCR-ABL), which is responsible for driving the disease through activation of downstream signal transduction pathways...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27902438/dna-double-strand-break-repair-is-involved-in-desiccation-resistance-of-sinorhizobium-meliloti-but-is-not-essential-for-its-symbiotic-interaction-with-medicago-truncatula
#2
Pierre Dupuy, Benjamin Gourion, Laurent Sauviac, Claude Bruand
The soil bacterium Sinorhizobium meliloti, a nitrogen-fixing symbiont of legume plants, is exposed to numerous stress conditions in nature, some of which cause the formation of harmful DNA double strand breaks (DSB). In particular, the reactive oxygen (ROS) and nitrogen (RNS) species produced during symbiosis, and the desiccation occurring in dry soils, are conditions which induce DSB. Two major systems of DSB repair are known in S. meliloti: homologous recombination (HR) and non-homologous end-joining (NHEJ)...
November 23, 2016: Microbiology
https://www.readbyqxmd.com/read/27896283/a-potential-founder-variant-in-carmil2-rltpr-in-three-norwegian-families-with-warts-molluscum-contagiosum-and-t-cell-dysfunction
#3
Hanne S Sorte, Liv T Osnes, Børre Fevang, Pål Aukrust, Hans C Erichsen, Paul H Backe, Tore G Abrahamsen, Ole B Kittang, Torstein Øverland, Shalini N Jhangiani, Donna M Muzny, Magnus D Vigeland, Pubudu Samarakoon, Tomasz Gambin, Zeynep H C Akdemir, Richard A Gibbs, Olaug K Rødningen, Robert Lyle, James R Lupski, Asbjørg Stray-Pedersen
BACKGROUND: Four patients from three Norwegian families presented with a common skin phenotype of warts, molluscum contagiosum, and dermatitis since early childhood, and various other immunological features. Warts are a common manifestation of human papilloma virus (HPV), but when they are overwhelming, disseminated and/or persistent, and presenting together with other immunological features, a primary immunodeficiency disease (PIDD) may be suspected. METHODS AND RESULTS: The four patients were exome sequenced as part of a larger study for detecting genetic causes of primary immunodeficiencies...
November 2016: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/27895125/lineage-specific-soxr-mediated-regulation-of-an-endoribonuclease-protects-non-enteric-bacteria-from-redox-active-compounds
#4
Jisun Kim, Chulwoo Park, James A Imlay, Woojun Park
Bacteria use redox-sensitive transcription factors to coordinate responses to redox stress. The [2Fe-2S] cluster-containing transcription factor SoxR is particularly tuned to protect cells against redox-active compounds (RACs). In enteric bacteria, SoxR is paired with a second transcription factor, SoxS, that activates downstream effectors. However, SoxS is absent in non-enteric bacteria, raising questions as to how SoxR functions. Here, we first show that SoxR of Acinetobacter oleivorans displayed similar activation profiles in response to RACs as did its homolog from Escherichia coli, but controlled a different set of target genes, including sinE, which encodes an endoribonuclease...
November 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27881779/allergic-inflammation-leads-to-neuropathic-pain-via-glial-cell-activation
#5
Ryo Yamasaki, Takayuki Fujii, Bing Wang, Katsuhisa Masaki, Mizuho A Kido, Mari Yoshida, Takuya Matsushita, Jun-Ichi Kira
: Allergic and atopic disorders have increased over the past few decades and have been associated with neuropsychiatric conditions, such as autism spectrum disorder and asthmatic amyotrophy. Myelitis presenting with neuropathic pain can occur in patients with atopic disorder; however, the relationship between allergic inflammation and neuropathic pain, and the underlying mechanism, remains to be established. We studied whether allergic inflammation affects the spinal nociceptive system...
November 23, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27877115/insights-into-brain-architectures-from-the-homological-scaffolds-of-functional-connectivity-networks
#6
Louis-David Lord, Paul Expert, Henrique M Fernandes, Giovanni Petri, Tim J Van Hartevelt, Francesco Vaccarino, Gustavo Deco, Federico Turkheimer, Morten L Kringelbach
In recent years, the application of network analysis to neuroimaging data has provided useful insights about the brain's functional and structural organization in both health and disease. This has proven a significant paradigm shift from the study of individual brain regions in isolation. Graph-based models of the brain consist of vertices, which represent distinct brain areas, and edges which encode the presence (or absence) of a structural or functional relationship between each pair of vertices. By definition, any graph metric will be defined upon this dyadic representation of the brain activity...
2016: Frontiers in Systems Neuroscience
https://www.readbyqxmd.com/read/27869829/contribution-of-copy-number-variants-to-schizophrenia-from-a-genome-wide-study-of-41-321-subjects
#7
(no author information available yet)
Copy number variants (CNVs) have been strongly implicated in the genetic etiology of schizophrenia (SCZ). However, genome-wide investigation of the contribution of CNV to risk has been hampered by limited sample sizes. We sought to address this obstacle by applying a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. A global enrichment of CNV burden was observed in cases (odds ratio (OR) = 1.11, P = 5.7 × 10(-15)), which persisted after excluding loci implicated in previous studies (OR = 1...
November 21, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27859919/integrated-multimodal-network-approach-to-pet-and-mri-based-on-multidimensional-persistent-homology
#8
Hyekyoung Lee, Hyejin Kang, Moo K Chung, Seonhee Lim, Bung-Nyun Kim, Dong Soo Lee
Finding underlying relationships among multiple imaging modalities in a coherent fashion is one of the challenging problems in multimodal analysis. In this study, we propose a novel approach based on multidimensional persistence. In the extension of the previous threshold-free method of persistent homology, we visualize and discriminate the topological change of integrated brain networks by varying not only threshold but also mixing ratio between two different imaging modalities. The multidimensional persistence is implemented by a new bimodal integration method called 1D projection...
November 17, 2016: Human Brain Mapping
https://www.readbyqxmd.com/read/27853540/persistent-homology-in-graph-power-filtrations
#9
Allen D Parks, David J Marchette
The persistence of homological features in simplicial complex representations of big datasets in R (n) resulting from Vietoris-Rips or Čech filtrations is commonly used to probe the topological structure of such datasets. In this paper, the notion of homological persistence in simplicial complexes obtained from power filtrations of graphs is introduced. Specifically, the rth complex, r ≥ 1, in such a power filtration is the clique complex of the rth power G(r) of a simple graph G. Because the graph distance in G is the relevant proximity parameter, unlike a Euclidean filtration of a dataset where regional scale differences can be an issue, persistence in power filtrations provides a scale-free insight into the topology of G...
October 2016: Royal Society Open Science
https://www.readbyqxmd.com/read/27847869/dysfunctional-mnsod-leads-to-redox-dysregulation-and-activation-of-prosurvival-akt-signaling-in-uterine-leiomyomas
#10
Vania Vidimar, David Gius, Debabrata Chakravarti, Serdar E Bulun, Jian-Jun Wei, J Julie Kim
AKT signaling promotes cell growth and survival and is often dysregulated via multiple mechanisms in different types of cancer, including uterine leiomyomas (ULMs). ULMs are highly prevalent fibrotic tumors that arise from the smooth muscular layer of the uterus, the myometrium (MM). ULMs pose a major public health issue because they can cause severe morbidity and poor pregnancy outcomes. ‬We investigate the mechanisms driving ULM growth and survival via aberrant activation of AKT. We demonstrate that an acetylation-mediated impairment of the manganese superoxide dismutase (MnSOD) activity is prevalent in ULM cells compared to the normal-matched MM from the same patients...
November 2016: Science Advances
https://www.readbyqxmd.com/read/27835694/occult-hbv-infection-in-immunized-neonates-born-to-hbsag-positive-mothers-a-prospective-and-follow-up-study
#11
Ying Lu, Ya-Lin Liu, Jing-Jing Nie, Xiao-Feng Liang, Ling Yan, Fu-Zhen Wang, Xiang-Jun Zhai, Jian-Xun Liu, Feng-Cai Zhu, Zhan-Jun Chang, Jie Li
OBJECTIVE: Occult HBV infection (OBI) has been reported in infants born to HBsAg-positive mothers despite immunization. This study aims to determine the maintenance of this status in a prospective birth cohort. METHODS: A total of 158 neonates born to HBsAg-positive mothers were enrolled. All received passive-active immunization against HBV according to a 0-1-6 schedule. Sera were collected at 7 months of age. Those diagnosed with OBI were serially followed up at 12, 24 and 36 months of age...
2016: PloS One
https://www.readbyqxmd.com/read/27830736/viral-vector-vaccines-expressing-nucleoprotein-and-phosphoprotein-genes-of-avian-bornaviruses-ameliorate-homologous-challenge-infections-in-cockatiels-and-common-canaries
#12
Marita Olbert, Angela Römer-Oberdörfer, Christiane Herden, Sara Malberg, Solveig Runge, Peter Staeheli, Dennis Rubbenstroth
Avian bornaviruses are causative agents of proventricular dilatation disease (PDD), an often fatal disease of parrots and related species (order Psittaciformes) which is widely distributed in captive psittacine populations and may affect endangered species. Here, we established a vaccination strategy employing two different well described viral vectors, namely recombinant Newcastle disease virus (NDV) and modified vaccinia virus Ankara (MVA) that were engineered to express the phosphoprotein and nucleoprotein genes of two avian bornaviruses, parrot bornavirus 4 (PaBV-4) and canary bornavirus 2 (CnBV-2)...
November 10, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27815383/persistence-of-wild-type-japanese-encephalitis-virus-strains-cross-neutralization-five-years-following-je-cv-immunization
#13
Emmanuel Feroldi, Mark Boaz, Sutee Yoksan, Kulkanya Chokephaibulkit, Usa Thisyakorn, Chitsanu Pancharoen, Céline Monfredo, Alain Bouckenooghe
BACKGROUND:  The live-attenuated Japanese encephalitis (JE) vaccine (JE-CV; IMOJEV(®)) induces a protective response in children. A shift in circulating JE virus strains suggests that a genotype shift phenomenon may occur throughout South-East Asia. We assessed the neutralization of wild-type (WT) JE virus isolates at distal time points post-vaccination. METHODS:  We analysed serum samples from a subset of 47 children who had received a JE-CV booster after an inactivated JE vaccine primary immunization...
November 3, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27814377/antibody-persistence-and-booster-responses-to-split-virion-h5n1-avian-influenza-vaccine-in-young-and-elderly-adults
#14
Rajeka Lazarus, Sarah Kelly, Matthew D Snape, Corinne Vandermeulen, Merryn Voysey, Karel Hoppenbrouwers, Annick Hens, Pierre Van Damme, Stephanie Pepin, Isabel Leroux-Roels, Geert Leroux-Roels, Andrew J Pollard
: Avian influenza continues to circulate and remains a global health threat not least because of the associated high mortality. In this study antibody persistence, booster vaccine response and cross-clade immune response between two influenza A(H5N1) vaccines were compared. Participants aged over 18-years who had previously been immunized with a clade 1, A/Vietnam vaccine were re-immunized at 6-months with 7.5 μg of the homologous strain or at 22-months with a clade 2, alum-adjuvanted, A/Indonesia vaccine...
2016: PloS One
https://www.readbyqxmd.com/read/27806927/molecular-mechanisms-of-bacterial-persistence-and-phenotypic-antibiotic-resistance
#15
Cui Peng, Xu Tao, Zhang Wenhong, Zhang Ying
Bacterial persistence refers to a state of reduced metabolic activity that endows a subpopulation of isogenic bacteria with multidrug tolerance. Persisters are phenotypic variants but not mutants. Since its discovery in 1944, bacterial persistence has not received enough attention until recently when its implications in persistent infections and biofilm infections become apparent. Much research has been done in recent years to investigate the mechanisms underlying bacterial persistence and phenotypic antibiotic resistance...
October 20, 2016: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/27805032/understanding-the-immune-system-architecture-and-transcriptome-responses-to-southern-rice-black-streaked-dwarf-virus-in-sogatella-furcifera
#16
Lin Wang, Nan Tang, Xinlei Gao, Dongyang Guo, Zhaoxia Chang, Yating Fu, Ibukun A Akinyemi, Qingfa Wu
Sogatella furcifera, the white-backed planthopper (WBPH), has become one of the most destructive pests in rice production owing to its plant sap-sucking behavior and efficient transmission of Southern rice black-streaked dwarf virus (SRBSDV) in a circulative, propagative and persistent manner. The dynamic and complex SRBSDV-WBPH-rice plant interaction is still poorly understood. In this study, based on a homology-based genome-wide analysis, 348 immune-related genes belonging to 28 families were identified in WBPH...
November 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27793055/personalized-anticancer-therapy-selection-using-molecular-landscape-topology-and-thermodynamics
#17
Edward A Rietman, Jacob G Scott, Jack A Tuszynski, Giannoula Lakka Klement
Personalized anticancer therapy requires continuous consolidation of emerging bioinformatics data into meaningful and accurate information streams. The use of novel mathematical and physical approaches, namely topology and thermodynamics can enable merging differing data types for improved accuracy in selecting therapeutic targets. We describe a method that uses chemical thermodynamics and two topology measures to link RNA-seq data from individual patients with academically curated protein-protein interaction networks to select clinically relevant targets for treatment of low-grade glioma (LGG)...
October 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27764938/1-2-4-triazolidine-3-thiones-have-specific-activity-against-acinetobacter-baumannii-among-common-nosocomial-pathogens
#18
Brendan W Corey, Mitchell G Thompson, Lauren E Hittle, Anna C Jacobs, Edward A Asafo-Adjei, William M Huggins, Roberta J Melander, Christian Melander, Robert K Ernst, Daniel V Zurawski
Acinetobacter baumannii are Gram-negative bacilli that pose a constant threat to susceptible patients because of increased resistance to multiple antibiotics and persistence in the hospital environment. After genome analysis, we discovered that A. baumannii harbors genes that share homology to an enzymatic pathway that elongates long-chain fatty acids (LCFA) in fungi. Previously, 1,2,4-triazolidine-3-thiones (T-3-Ts) were shown to inhibit hyphae production in fungi, and this same LCFA elongation pathway was implicated as the possible target...
November 3, 2016: ACS Infectious Diseases
https://www.readbyqxmd.com/read/27760146/alignment-of-homologous-chromosomes-and-effective-repair-of-programmed-dna-double-strand-breaks-during-mouse-meiosis-require-the-minichromosome-maintenance-domain-containing-2-mcmdc2-protein
#19
Friederike Finsterbusch, Ramya Ravindranathan, Ihsan Dereli, Marcello Stanzione, Daniel Tränkner, Attila Tóth
Orderly chromosome segregation during the first meiotic division requires meiotic recombination to form crossovers between homologous chromosomes (homologues). Members of the minichromosome maintenance (MCM) helicase family have been implicated in meiotic recombination. In addition, they have roles in initiation of DNA replication, DNA mismatch repair and mitotic DNA double-strand break repair. Here, we addressed the function of MCMDC2, an atypical yet conserved MCM protein, whose function in vertebrates has not been reported...
October 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27733858/leaf-like-sepals-induced-by-ectopic-expression-of-a-short-vegetative-phase-svp-like-mads-box-gene-from-the-basal-eudicot-epimedium-sagittatum
#20
Zhineng Li, Shaohua Zeng, Yanbang Li, Mingyang Li, Erik Souer
Epimedium L. (Berberidaceae, Ranales), a perennial traditional Chinese medicinal herb, has become a new popular landscape plant for ground cover and pot culture in many countries based on its excellent ornamental characteristics and, distinctive and diverse floral morphology. However, little is known about the molecular genetics of flower development in Epimedium sagittatum. Here, we describe the characterization of EsSVP that encodes a protein sharing 68, 54, and 35% similarity with SVP, AGAMOUS-like 24 (AGL24) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) in Arabidopsis, respectively...
2016: Frontiers in Plant Science
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